roary -f OUTDIR is not honoured if OUTDIR exists

[tseemann]

It turns out that if you rerun roary with the same -f OUTDIR it will instead put the result in OUTDIR . EPOCH_SECONDS.

I feel this behaviour is helpful in some ways (not lose a big result) but harmful and confusing in others.

Either (1) error with "OUTDIR already exists" or (2) just overwrite it; or (3) allow overwriting with --force option.

PS. This is ISSUE 404 NOT FOUND?

[surh]

I also find this behavior problematic. I am trying to use roary with snakemake, but by defining the expected outputs snakemake creates the OUTDIR before running roary, which then creates OUTDIR/EPOCH_SECONDS.

I think adding a --force or --overwrite option is best